CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
416 lines
12 KiB
JSON
416 lines
12 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "prepare_multiqc_input",
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"description": "Prepare directory with all the input files for MultiQC.\n",
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"type": "object",
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"definitions": {
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"input" : {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"fail_trimming_multiqc": {
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"type":
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"string",
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"description": "Type: `string`. ",
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"help_text": "Type: `string`. "
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}
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,
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"fail_mapping_multiqc": {
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"type":
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"string",
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"description": "Type: `string`. ",
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"help_text": "Type: `string`. "
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}
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,
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"fail_strand_multiqc": {
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"type":
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"string",
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"description": "Type: `string`. ",
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"help_text": "Type: `string`. "
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}
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,
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"fastqc_raw_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"fastqc_trim_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"trim_log_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"sortmerna_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"star_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"salmon_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"samtools_stats": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"samtools_flagstat": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"samtools_idxstats": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"markduplicates_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"pseudo_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"featurecounts_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"featurecounts_rrna_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"aligner_pca_multiqc": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"aligner_clustering_multiqc": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"pseudo_aligner_pca_multiqc": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"pseudo_aligner_clustering_multiqc": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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,
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"preseq_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"qualimap_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"dupradar_output_dup_intercept_mqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"dupradar_output_duprate_exp_denscurve_mqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"bamstat_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"inferexperiment_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"innerdistance_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"junctionannotation_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"junctionsaturation_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"readdistribution_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"readduplication_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"tin_multiqc": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\",\"`. ",
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"help_text": "Type: List of `file`, multiple_sep: `\",\"`. "
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}
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,
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"multiqc_config": {
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"type":
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"string",
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"description": "Type: `file`. ",
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"help_text": "Type: `file`. "
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}
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}
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},
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"ouput" : {
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"title": "Ouput",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.output.output`. ",
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"help_text": "Type: `file`, default: `$id.$key.output.output`. "
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,
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"default": "$id.$key.output.output"
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}
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}
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},
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"nextflow input-output arguments" : {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
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"properties": {
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"publish_dir": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/input"
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},
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{
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"$ref": "#/definitions/ouput"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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